Kept in the Loop
by EternalFae
Summary: AU. How would Kaidan's character arc have progressed if Liara hadn't inexplicably left him in the dark?
1. Chapter 1

Chapter 1

*Three months before the attack on Freedom's Progress*

Kaidan Alenko was lost. Entire colonies where disappearing at a time. There was no sign of any conflict, as if everyone just got up and walked away in the middle of their routines. The Alliance was scrambling to find out what was going on and having no success. But there was more to it than that.

Kaidan's promotion to Staff Commander made him privy to more things that the brass didn't want the grunts or the general public to know; things like Lieutenant Commander John Shepard being alive and working for Cerberus. Kaidan wracked his mind for explanations, but no matter how hard he thought, no matter how many scenarios he went through, only one presented itself; if he really was alive, then John Shepard was a traitor. Why else would he have faked his death? Why else would it take him so long to resurface? And in the employ of a terrorist group? Kaidan didn't want to believe it, but he couldn't let his personal feelings distort what was right in front of him.

Councilor Anderson and Admiral Hackett were no help. Kaidan approached them both about what he was seeing, only to find himself suddenly stonewalled by his normally dependable superiors. He knew they were seeing the same reports. They had put up a good front, but they seemed plenty confused in their own right. If Shepard were on an undercover mission, the human councilor and one the Alliance's highest ranking admirals would not be kept in the dark, and even if they were, why have Shepard fake his death that way. Images of the _Normandy_ in flames suddenly flashed through Kaidan's mind.

Kaidan was snapped out of his musings by his communicator. It was Tina Venin, one of the base guards.

"Commander Alenko? There's an asari here _demanding_ to see you. Has been for the past hour. I tried to get her to leave, but she knows that she's not breaking any laws and she's refusing to go anywhere until I let her see you," the guard said angrily.

"Does this asari have a name?" Kaidan asked tersely. It was not the first time this guard had been a problem when it came to aliens.

"Dr. Liara T'soni, she says."

"Send her in immediately!" Kaidan barked. "And I'll be talking to your captain later about your treatment of non-humans visitors," Kaidan added more quietly.

"Y-yes, sir," Venin stammered.

Five minutes later, a very familiar asari walked into Kaidan's office.

"It's good to see you again, Kaidan," Liara said as she returned his hug.

"You too, Liara. Why are you here?"

"Unfortunately, this isn't a social call."

As Liara accepted Kaidan's silent offer to take a seat, she said, "Kaidan, there are things you need to know, a lot of them unbelievable, but I need you to promise to hear me all the way through."

"Of course."

"I know you've been getting reports about Shepard being alive. And working with Cerberus," Liara said bluntly.

"Liara, I-how could you possibly know about that?"

"For almost two years now, I've been working as an information broker on Ilium. I have sources in many places, including the Alliance. It is simply a matter of knowing who to talk to and how much to pay," she explained.

"So you know what's going on with Shepard?" Kaidan prompted. He didn't like the idea of anyone having moles in the Alliance, but if Liara had answers…

"About a month after he was killed," Liara began, "I got a tip that he was alive and on Omega. When I went to investigate, I instead found out that the Shadow Broker had retrieved his body and was trying to sell it. I saw it for myself. There is no doubt that Shepard was dead."

"Guess he didn't like Shepard keeping that info from him two years ago," Kaidan said dryly.

"Apparently not. He was trying to sell Shepard's body to the Collectors."

"I thought they were a myth," Kaidan interrupted.

"That's what they want everyone to think," Liara explained. "I suspect it is why they do not operate in stable regions of space. The Collectors are the ones who destroyed the _Normandy_. It appears that they hired the Shadow Broker to deliver Shepard's body to them so they could confirm that he was really dead."

"So how did Shepard go from being dead and in the Shadow Broker's hands to being alive and working with Cerberus?" Kaidan asked.

"Cerberus was looking for Shepard's body too," Liara said slowly. "They offered to help me save him from the Shadow Broker. There was little time and I could see no alternatives, so I accepted."

"But why didn't you bring his body back to the Alliance?"

"Cerberus said that they were developing technology that could bring him back. I know it's hard to believe, but if there was even a remote chance, I had to take it. The only alternative was to leave him dead for sure! So I…"

"So you gave his body to one of the Council and the Alliance's worst enemies," Kaidan said accusingly.

"I know it was beyond a long shot, but it may have worked," Liara said defensively. "You've seen the reports about Shepard being alive."

"That could just be Cerberus trying to manipulate us," Kaidan pointed out.

"But then why wait almost two years? Why would they need to recover Shepard's body for themselves if all they wanted was to manipulate the Alliance?" Liara demanded.

Kaidan realized that she had a point, but that was hardly enough to believe something so incredible.

"Even if they did… rebuild him, how can we be sure that Shepard is really himself? Control chips are not new technology. Or maybe they're just controlling his body with tech somehow." A small part of Kaidan started to hope that maybe what Liara was telling him was true, but he knew that accepting something like this at face value was extremely risky.

"The Illusive Man was very adamant that he, and all of us, need Shepard as he was, and I'm inclined to believe that he was telling the truth. It can't be a coincidence that only a month after we destroyed a Reaper, the Collectors appeared out of nowhere to kill the person who made it possible. If the Collectors aren't connected to the Reapers, then they had no reason to attack like that, so that must mean that the battle against Sovereign has the Reapers scared."

"That's a lot of supposition, Liara," Kaidan said.

"It's a big coincidence if it's not true," Liara retorted. "I know how much this all stretches credulity. The Illusive Man claims that Cerberus' ultimate goal is the advancement of humanity. I don't believe for a second that it stops there, especially not after what I saw when we raided their bases two years ago, but I believe it is at least a portion of the truth."

"Cerberus' human supremacist leanings are well-known within the Alliance," Kaidan conceded.

"Exactly, so whatever their goal is, it puts them in opposition to the Reapers. I think the husks we saw on Chasca two years ago were Cerberus' attempt to co-op Reaper technology for their own use, like Saren attempted at first. So regardless of their real motives, I believe the human saying, 'the enemy of my enemy is my friend' applies here," said Liara.

"_If_ this is all true," Kaidan clarified. "I'll need to see Shepard for myself, or at least hear from someone else who did, before I really believe it. But I think there's enough to work around the possibility. First things first, what are your plans after you leave?"

"I have a ship scheduled to leave for Tuchanka tomorrow," Liara explained, relieved that Kaidan trusted Liara enough to act on what she was telling him, even if he didn't fully believe it. "Getting Wrex to talk to me should not be a problem. Next is Tali; convincing the Admiralty Board to let me talk to her could be difficult. Finding Garrus will be the most difficult step, so I'm saving him for last. Hopefully it won't cause any problems if I can't find him. I thought I should talk to you first because your position in the Alliance would make you more vulnerable to the Illusive Man's efforts to isolate Shepard from us. I will also be hunting down the Shadow Broker. He is clearly not an ally against the Reapers, and he needs to pay for what he's done. What will you be doing?" Liara asked.

"I think I might be able to convince Anderson or Hackett to send me on an "infiltration" mission, to ascertain Shepard's actions. It will just cause more problems if I desert. If that doesn't work, I can at least collect useful intel," Kaidan said.

"Good," Liara said. She tapped a few keys on her omni-tool to send something to Kaidan's.

"This is a code we'll all send to each other if one of us confirms that Shepard is really alive, as well as how much control Cerberus seems to have over him. And Kaidan… thank you. I know it takes a lot of trust to even consider all the things I've told you."

Kaidan thought about the lengths Liara was going to for Shepard.

"After hearing all this Liara, I have to ask. Where you and Shepard…" Kaidan trailed off.

"He turned me down," Liara answered sadly.

"I'm sorry."

"It's all right. I… can't control other people's feelings."

When Liara stood to leave, Kaidan hugged her again. They said their goodbyes and promised to keep each other updated. Alone in his office again, Kaidan immediately went to his terminal to send a message. He needed to speak to the admiral.

AN: I firmly believe that if this conversation had happened in canon, things would have gone very differently.


	2. Chapter 2

Chapter 2

"You're talking to a legend. And a ghost."

Commander Shepard didn't know what to expect when he saw Kaidan again. His face was a little more worn, and he was beginning to develop some grey around his temples, but Shepard would still recognize him anywhere.

"This wasn't how I expected us to run into each other," Kaidan said as he shook Shepard's hand. "It's good to see you too, Garrus." Garrus nodded.

"You expected to run into me?" Shepard asked.

"The Alliance has been getting reports of you being alive for months now."

"So much for security," Miranda interjected.

Kaidan ignored her. "The reports are pretty ugly. To someone who doesn't know the whole story, it looks like you faked your death and turned traitor."

"I gathered as much when I talked to Anderson and the council."

"I'm not sure you realize just how bad it is," Kaidan replied. "There are things you need to know and I'd rather not discuss it with anyone from Cerberus in earshot."

"We've given Shepard everything he needs," Miranda retorted.

"I'll be the judge of that Miranda!" Shepard snapped.

"I'll make sure she stays put while the two of you talk," Garrus suggested.

"You sure?" Kaidan asked. "It would be a good idea for you to know these things too."

"Shepard can fill me in later."

Kaidan nodded and motioned for Shepard to follow him. Miranda did not look happy.

Once Garrus and Miranda were out of sight and out of earshot, Shepard said, "I can't help but notice that Garrus is the only member of the crew that was surprised to see me alive. Joker and Chakwas I can understand; they wouldn't have joined Cerberus if they hadn't told them, but what about you and Tali?"

"How much did Cerberus tell you about how they got your body?" Kaidan asked.

"Not much. What does that have to do with anything?"

"I need to get a feel for what they've been telling you," Kaidan began. "About a month after you were killed, Liara got a tip that you were alive and on Omega. It was fake, obviously. Instead, she found out that the Shadow Broker had retrieved your body and was trying to sell it to the Collectors."

"Why would the Collectors want my body?" Shepard interrupted.

"We think they were trying to confirm that you were really dead."

"One more thing," Shepard said before Kaidan could continue. "When I asked the Illusive Man about the rest of you, he said that Liara had become one of the Shadow Broker's agents. Why would Liara do that if she had to fight him for my body?"

"He lied to you," Kaidan replied bluntly. "That's good to know though. It confirms our suspicions that he's trying to isolate you from the rest of us. Liara isn't working for the Shadow Broker. Quite the opposite in fact; she's trying to kill him."

"And how did Cerberus get involved?" Shepard asked.

"They ran into Liara while they were searching for your body themselves and offered to help," Kaidan explained. "Once you were successfully recovered, they told Liara that they were working on technology that could bring you back. She knew it was beyond a long shot, but she took it. You'll have to talk to Liara herself about her reasons."

"And how did you and Tali find out?" Shepard asked.

"Wrex knows too," Kaidan started. "About three months before the Collectors took Freedom's Progress, the Alliance started getting the reports I mentioned earlier. They talked about things like various Cerberus projects you were participating in; had been participating in for quite some time. If I hadn't found out what was really going on…" Kaidan shook his head. "About a week after the reports started appearing, Liara came to visit me. She told me everything that I told you."

Shepard interrupted. "How did Liara even know about the reports?"

"For the last two years, she's been an information broker on Illium. She said it was just a matter of knowing which palms to grease. She came to talk to me immediately because she suspected that the Illusive Man would try to isolate you, and that my position in the Alliance could make me more vulnerable. I didn't fully believe her at first. Someone coming back from the dead? It just seemed so… incredible. I'm still having trouble wrapping my head around it."

"Try experiencing it directly," Shepard retorted darkly.

"Sorry. It didn't occur to me that…"

"It's okay," Shepard said apologetically. "I'm… just trying not to think about it at all."

"Anyway," Kaidan continued. "She went to Tuchanka next. Getting Wrex to talk to her wasn't hard. Tali was a bit trickier because of the Admiralty board, but Liara got through eventually. She tried to find Garrus to fill him in too, but no one knew where to start looking. We were worried it might cause problems with him. It's good to see that's not the case. After Tali met you on Freedom's Progress, she sent us all a coded message confirming that you were alive and not following Cerberus' orders."

"Cerberus didn't tell me any of those things," Shepard said.

"I'm not surprised. You mentioned Dr. Chakwas earlier. Did you have her examine you?"

"Yeah. She didn't find anything that looked like a control device. I suppose they could have come up with one that she couldn't find, but Miranda Lawson, the director of Project Lazarus, actually seemed upset that she wasn't allowed to put in a control chip. She could have been lying of course, but she strikes me as being too proud to fake pouting," Shepard explained.

"Guess the Illusive Man is confidant in his ability to manipulate you the old-fashioned way," Kaidan observed.

"Looks like," Shepard agreed. "I appreciate you telling me all this. There's something else I need to know; can you come with me?"

"I want to Shepard," Kaidan said. "But I can't. When Liara first told me what was going on, I tried to talk Anderson and Hackett into sending me to "investigate" you. They both said no. Even with everything our people sacrificed two years ago, there are still factions in the other species that are waiting for any chance to jump on us. If the Alliance shows even the slightest sign of sympathizing with Cerberus it would turn into a political nightmare. Anderson, Hackett, and I are already pushing things just keeping the Alliance and council from interfering with you."

"And if you joined me anyway, you'd be charged with treason and desertion," Shepard conceded. "I don't suppose you could get a leave of absence."

Kaidan shook his head. "Now that we've talked, I'd be put under suspicion just for asking."

"It won't feel right doing this without you," Shepard said sadly.

"I know, but someone needs to look at the long term while you deal with the Collectors. Just… be careful. I believe in you, but I don't trust Cerberus any further than I can throw them without my biotics," Kaidan warned.

"Neither do I," Shepard said.

"Okay. I… need to go make my reports. If I find anything that might be able to help you, I'll let you know," Kaidan said quietly.

"Kaidan," Shepard put a hand on Kaidan's shoulder. "I'll come back this time. I promise."

"I'll hold you to that."

Neither man looked back as they parted ways. Shepard wanted Kaidan with him so badly, but it was enough to know that he was still looking out for him. Garrus intercepted Shepard as he got back.

"How did it go?" he asked.

"About as well as it could, all things considered. He can't join us, but he'll still try to help out."

Garrus just nodded as Shepard activated his communicator.

"Come pick us up Joker. I've had enough of this place."


	3. Chapter 3

Chapter 3

*Shortly after recruiting Thane and Samara*

_Commander Shepard_

_I have intel that may be relevant to your mission._

_Meet me on the Citadel. I will transmit my exact coordinates to your omni-tool when you arrive. Rest assured that it will be in a public space._

_You are welcome to bring backup if you feel you must. Just be sure that anyone accompanying you has no association with your current employer._

_I look forward to seeing you._

"EDI, can you trace the message I just closed back to its sender?" Shepard asked.

"Give me a moment," EDI replied. "Done. It came from a public terminal on the Citadel. The terminal was hacked to remove the identification requirement. Without access to time-stamped security footage from the Citadel, it is not possible to ascertain the identity of the sender."

"Thanks," Shepard said. "We need to go to the Citadel anyway. Set the course, Joker."

"Aye-aye, Commander."

As the _Normandy _flew to the Citadel, Shepard retreated to his cabin to go over the latest mission reports. About an hour before they arrived, Miranda walked in.

"Shepard, Yeoman Chambers told me about the message you received a few hours ago. The one that cannot be traced to anyone and told you not to bring any backup associated with Cerberus. Do you really think it is wise to meet this person?" Miranda asked.

"He didn't say I couldn't bring any backup at all," Shepard pointed out. "And he said that the meeting would be in a public place."

"To make it easier to abduct you in plain sight?" Miranda suggested.

"What do you take me for, Miranda?"

"Shepard…"

"I know you don't like it, Miranda," Shepard began. "But if it gets us more intel on the Collectors, it's worth the risk. I've already decided to bring Garrus and Tali with me to be safe."

"And if that's not enough?" Miranda asked.

"I've been in much worse situations. So have Garrus and Tali," Shepard pointed out.

"That doesn't' guarantee your ability to escape any you encounter in the future. What if…"

"Look, Miranda," Shepard interrupted. "If you really want me to trust Cerberus, you need to give me some freedom to get help from other sources. This one has gone out of his way to give me a reason to trust him without actually revealing who he is. We'll know more when we get to the Citadel and he tells me where to meet. If there's something suspicious about the meeting place, then I'll think about taking more backup. Until then, I've ordered EDI to alert me if someone else leaves the ship and if I find out that someone has hacked into my omni-tool there will be hell to pay."

"Very well, Commander," Miranda said tightly. After she stalked out of the captain's cabin, Shepard just rolled his eyes and went back to his datapads.

When Shepard walked onto the dock, flanked by Garrus and Tali, his omni-tool pinged immediately. Shepard raised an eyebrow when he saw the coordinates. Why would his source want to meet him there?

Shepard went to the upper wards as he was told. When he saw the familiar sight of the Citadel's arms stretching before him, he couldn't help but think of the last time he was here. His eyes traveled to the viewpoint, where he noticed a familiar dark-haired human leaning on the fence. Shepard moved to join him as Garrus and Tali positioned themselves to watch for any listeners.

"Shepard."

"Kaidan. So… what's with the 'cloak and dagger' routine?"

"I wanted to give Cerberus as little ammo as possible," Kaidan explained.

"Fair enough. Why here?" Shepard couldn't help but ask.

"I thought you'd be more likely to come if you had some sort of hint about who you would be talking to, and Cerberus has no reason to think this place means anything to us."

"Doesn't feel like it's been two years," Shepard said sadly.

"I guess it wouldn't to you. To be honest, the extra time hasn't made it much easier for me either," Kaidan said.

"I can't help but wonder what Ash would think of all this."

"I imagine she'd be raising hell with the brass," Kaidan said with a laugh.

"Sounds like her. Speaking of the brass, have they done anything with your report on Horizon?" Shepard asked.

"They're convinced that the Collectors are a threat now," Kaidan began. "They've started looking more seriously into countermeasures. Though they're also using the husks as an excuse to pin this on the geth instead of acknowledging the Reapers."

"Figures," Shepard said tersely. "What kind of countermeasures are they thinking about?"

"A contact in R&D tells me that they're looking into repelling the seekers with shields and biotic barriers. They're using the footage recovered from Horizon to figure out the right frequency."

"They really think that will work?" Shepard asked.

"In theory. It's not exactly something that can be easily tested," Kaidan pointed out.

"I'll keep it in mind just the same," Shepard said.

"So… about the real reason I called you here," Kaidan began.

"I knew it wasn't just to reminisce and give me a sit-rep."

"No, it wasn't," Kaidan agreed. "I've been given a mission. A Blue Suns team on the planet Joab has uncovered a Prothean beacon."

"A beacon?!" Shepard asked, startled.

"Yeah. I've been assigned to take a team in and recover it. The council wants it for study of course, but it won't be much use without the Cipher. That's where you come in," Kaidan said.

"What makes you think this beacon will tell me anything the other two didn't?"

"I took a few scans of the Virmire beacon after you used it," Kaidan began. "It was in better shape than the one on Eden Prime, but there was still a lot of damage. It was dumb luck that the information on Ilos was still in there. You still don't have the full message. Preliminary reports on the Joab beacon say that it's in better shape than the other two, so it should have at least some of the missing pieces."

"And you think the extra information involves the Collectors somehow?"

"The Collectors are servants of the Reapers. It's possible that the Protheans knew about them and included it in their warning."

"It's a long shot," Shepard said.

"I know, but we need all the leads we can get. Even if it doesn't include anything about the Collectors specifically, it could still give you something that could help, either against the Collectors or the Reapers themselves."

"How is this going to work?" Shepard asked.

"I have about three days to prep my team. That should give you enough time to go in, get the message from the beacon, and get out before anyone knows you were there. Then I come in and bring the beacon back to the Citadel without anyone knowing the difference," Kaidan explained.

"The Blue Suns won't give up something like a beacon easily," Shepard pointed out. "Should I expect anything different from them?"

"They'll have brought in some of their most elite troops, but no unusual tricks."

"I appreciate this, Kaidan," Shepard said as Kaidan sent the exact coordinates to Shepard's omni-tool.

"Just make it count," Kaidan replied. "I need to go start my preparations. Tell Garrus and Tali I said 'hi.'" With that, Kaidan walked away.

As Kaidan vanished into the crowd, Shepard motioned for Garrus and Tali to follow him. They left to talk Captain Bailey about Fade. Once their business on the Citadel was complete, they would find out what was missing from the Eden Prime and Virmire beacons.

a/n: This AU also applies on the meta level. I figure that since Liara and Wrex both helped with sidequests, Kaidan would have too. In this scenario, completing the mission on Joab would trigger the Collector Ship mission.


End file.
